18-64055666-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649298.1(LINC01924):n.675+13437A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,150 control chromosomes in the GnomAD database, including 44,279 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (44279 hom., cov: 32)
• Consequence: LINC01924 ENST00000649298.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

LINC01924 (HGNC:27600): (long intergenic non-protein coding RNA 1924)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01924	ENST00000649298.1	n.675+13437A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115644 AN: 152032 Hom.: 44251 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.779

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.761 AC: 115717 AN: 152150 Hom.: 44279 Cov.: 32 AF XY: 0.768 AC XY: 57099 AN XY: 74378

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.782

Alfa AF: 0.732 Hom.: 5103

Bravo AF: 0.771

Asia WGS AF: 0.896 AC: 3114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.5
Dann	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8094641; hg19: chr18-61722900;